Plasmonic lens is a key component in the development of sub-wavelength resolution optical system for bio-imaging and nanolithography applications. In order to develop a deterministic fabrication capability for nanostructures on plasmonic lens by using focused ion beam, this paper presents a highly robust and accurate surface topography model based on level set method. Sputtered atom distribution and angular dependence of sputter yield are calculated by Monte Carlo simulation programs SRIM/TRIM and TRIDYN, respectively. Redeposition effect is included in the physical model and successfully embedded into a topography simulation program by applying the level set method. The proposed model is validated and evaluated in the focused ion beam fabrication experiments. Simulation error of less than 7% is obtained. Two types of nanostructures for plasmonic lens were fabricated using the machining parameters approved by this simulation model. Simulation errors of 7 and 2 nm were found in a nanodots array and a spiral Bragg grating, respectively. The results clearly demonstrate the effectiveness of the modelling approach developed for deterministic fabrication of nanostructures